RNA Detection

from miRBase, and/or nonredundant RNAs from the human

transcriptome annotations as references. After mapping reads

to these references, chiastic reads were assembled into duplex

groups and filtered to remove interactions within RNAs and

ones with identical break points. Normal gapped reads are not

used since these are all for RNA structures, not RNA–RNA

interactions. The remaining chiastic reads are used to identify

RNA–RNA interactions.

7. To visualize the interaction between a pair of RNAs, use the
   following script. This analysis produces a pair of tracks for the
   interacting RNAs, highlighting the regions involved in interac-
   tion (seeFig. 6 for two examples). The SAM files from the
   previous step are used as the input. Parameters are defined
   within the following script.

python intrxn_specificity.py

80 100

human SNORD16

mouse SNORD16 mouse U6

human U6

80

hu

SNORD16 box D U6(potential methylation)

**** C77

CGUAAUUUGCGUCUUACUCUGUUCUCAGCGAC&GCGCAAGGAUGACACGCAAAUUCGUG

...(((((((((.(((.(..............&.......).))).)))))))))....

A

B

25 30

25

20

15

10

5

0

0204060

20

15

SNORD16:U6coverage (HEK)

SNORD16:U6coverage (mES) SNORD16:U6coverage (mES)

SNORD16:U6coverage (HEK)

10

5

0

0

1

2

3

4

5

6

7

8

9

0

1

2

3

4

5

6

7

8

9

0

0 20 40 60 80 0 20 40 60 80 100

20 40 60 80

Fig. 6Analysis and visualization of a new interaction between SNORD16 (or U16) and U6 in human HEK 293T
cells and mouse ES cells. (a) Thebluehighlighted regions are the sequences involved in base pairing. (b) The
interaction model. Box D is a characteristic sequence motif in the C/D box snoRNAs. SNORD16 is known to
guide modification of 18S rRNA (snoRNABase) [30]. Here, we show that it may also guide the modification of
U6 snRNA at C77, the same site as the SNORD10 target (snoRNABase) [31], but the base pairing is less perfect
compared to the SNORD10–U6 interaction. For more examples,seeFig. 5 and Fig. S6 the PARIS paper [21]

PARIS: Psoralen Analysis of RNA Interactions and Structures 79